[WIP] Reorganize and update documentation #5059

OriolAbril · 2021-10-08T15:22:38Z

will close #4044 and will close #4894

what are the (breaking) changes that this PR makes? This will break a lot of links as once merged, latest (and after release stable) will stop having notebooks build within the docs, many pages will be renamed or moved...
important background, or details about the implementation. This is key GSoD work which also build on top of recent improvements around notebooks and versioned docs.
linting/style checks have been run
right before it's ready to merge, mention the PR in the RELEASE-NOTES.md. This will change the face of the website considerably, so it would be great to sync with major 4.0 release and advertize improved docs with the release

martinacantaro · 2021-10-09T05:58:08Z

Still working on it, many TO-DOs and things to be fixed

OriolAbril

quick review, tried to focus on fail fast comments on things that I think you are probably following the wrong path or lack some context. Hopefully this will prevent you from spending too much time on things that then need to be changed

docs/source/community.md

docs/source/index.md

OriolAbril · 2021-10-09T18:23:19Z

docs/source/index.md

+
+# Citing PyMC
+
+Use this to cite the library:


cc @michaelosthege we should probably add a mention to zenodo somewhere I think

We mention it on the Github landing page IIRC

Zenodo is only mentioned like this in the readme: DOIs for specific versions are shown on Zenodo and under Releases

docs/source/installation.md

twiecki · 2021-10-09T18:53:00Z

Where do the conflicts come from?

Also, is there a place to see what it'd look like?

OriolAbril · 2021-10-09T19:02:19Z

Where do the conflicts come from?

I started setting this up 1-2 months ago so it's probably renaming changes.

Also, is there a place to see what it'd look like?

Yes, all PRs have a preview of how will their docs look like, you have to search for the readthedocs check, wait until it finishes and click "Details"

michaelosthege · 2021-10-09T19:43:31Z

While you're at it, can you fix the coverage badge link on the docs landing page?

codecov · 2021-10-10T03:54:09Z

Codecov Report

Merging #5059 (8476e53) into main (140dab0) will increase coverage by 0.85%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #5059      +/-   ##
==========================================
+ Coverage   78.08%   78.94%   +0.85%     
==========================================
  Files          88       88              
  Lines       14171    14248      +77     
==========================================
+ Hits        11066    11248     +182     
+ Misses       3105     3000     -105

Impacted Files	Coverage Δ
pymc/step_methods/hmc/integration.py	`78.84% <0.00%> (-3.85%)`	⬇️
pymc/bart/pgbart.py	`95.14% <0.00%> (-1.10%)`	⬇️
pymc/parallel_sampling.py	`86.33% <0.00%> (-1.00%)`	⬇️
pymc/step_methods/hmc/nuts.py	`95.00% <0.00%> (-0.63%)`	⬇️
pymc/tests/sampler_fixtures.py	`90.76% <0.00%> (-0.48%)`	⬇️
pymc/aesaraf.py	`89.70% <0.00%> (-0.41%)`	⬇️
pymc/distributions/multivariate.py	`71.34% <0.00%> (-0.13%)`	⬇️
pymc/gp/cov.py	`98.07% <0.00%> (ø)`
pymc/sampling_jax.py	`0.00% <0.00%> (ø)`
pymc/backends/arviz.py	`89.55% <0.00%> (ø)`
... and 11 more

aloctavodia · 2021-10-11T05:41:20Z

docs/source/api.rst

+   api/smc
+   api/step_methods
+   api/inference
+   api/plots


Now we have a BART module #5058

Cool, I was going to ask more questions about the api resources, including BART, because we've been talking a bit with @OriolAbril about what needs to be displayed for users, what needs to be displayed for devs and what doesn't need to be displayed at all.
We were basing the current API tree on the Architecture diagram, but that is probably out of date (as evidenced by it not including BART).
What other things should be included/excluded?
For example, does logprob submodule in distributions need to be added?

Adding comment by @Sayam753 :

Yes. At least, logp and logcdf functions should be exposed

conda-envs/environment-dev-py37.yml

docs/source/learn/notebooks.md

review-notebook-app · 2021-11-13T18:14:23Z

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example doc restructure working and hopefully illustrative doc skeleton update requirements WIP Change log: - Upload new PyMC logo - Updated conf.py to pymc instead of pymc3 - Start configuring and populating index page - Start configuring and populating learning page - Start configuring and populating api page - Updated API to follow the docs/Architecture.png layout - Start configuring and populating learning page - Fix typo in filename of "index legacy" add community page, other minor changes Continue restructuring the API Delete conflicting files example doc restructure update requirements update requirements and gitignore some fixes add changes introduced by pre-commit checks fix community page title update api for distributions update gaussian process api fix end of file more changes sponsor logos sponsor logos cleanup, other changes changes to satisfy pre-commit checks requirements changes minor changes Add testimonials to docs homepage remove sphinx panels and other changes center buttons add explanation of MAP to glassor minor change fix typo minor changes put content in videos and podcasts section. Change formatting of testimonials (width of 2 cards for better formating in narrow screens) add code example to front page revise some definitions (#5126) minor changes minor changes WIP: organizing notebooks into learning section

docs/source/Advanced_usage_of_Aesara_in_PyMC.rst

- Add information for institutions in the Contributing section - Center navbar - Split the About section into a main page with multiple subpages - Remove old reference to "developers" in the index toctree

Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com>

docs/source/about/citing_pymc.md

OriolAbril · 2021-11-16T09:25:59Z

docs/source/about/citing_pymc.md

+
+.. code-block:: none
+
+    @article{pymc,


Looks like doi is missing here comparing with citation above

OriolAbril · 2021-11-16T09:27:27Z

docs/source/about/citing_pymc.md

+      pages={e55},
+      year={2016},
+      publisher={PeerJ Inc.}
+    }


Add todo or note on clickup (might be done already) about adding zenodo here, the readme on pyms repo has the right citation info

OriolAbril · 2021-11-16T09:28:24Z

docs/source/about/pymc_for_enterprise.md

+let's face it, amazing!
+
+
+TODO fix code


More than fix ckde, use sphinx design buttons. Otherwise the next time bootstrap is updated the buttons will break again

OriolAbril · 2021-11-16T09:30:20Z

docs/source/conf.py

    "notfound.extension",
+    "sphinx_design",


Sphinx desing looks duplicated

docs/source/contributing/jupyter_style.md

docs/source/index.md

OriolAbril assigned martinacantaro Oct 8, 2021

OriolAbril marked this pull request as draft October 8, 2021 15:22

martinacantaro force-pushed the doc_skeleton_update branch from 7d2a793 to ec50e41 Compare October 9, 2021 05:53

OriolAbril commented Oct 9, 2021

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OriolAbril force-pushed the doc_skeleton_update branch from edd7649 to b1629f3 Compare October 10, 2021 03:40

martinacantaro force-pushed the doc_skeleton_update branch from b1629f3 to bbfb3da Compare October 10, 2021 03:44

OriolAbril force-pushed the doc_skeleton_update branch from bbfb3da to 630f021 Compare October 10, 2021 04:06

aloctavodia reviewed Oct 11, 2021

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martinacantaro force-pushed the doc_skeleton_update branch 2 times, most recently from dfce56c to 667d83b Compare October 12, 2021 00:40

OriolAbril commented Oct 16, 2021

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OriolAbril commented Nov 13, 2021

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OriolAbril force-pushed the doc_skeleton_update branch from a6e8ad3 to 2c65116 Compare November 13, 2021 18:47

OriolAbril and others added 5 commits November 13, 2021 21:28

add style guides

71e342e

remove multilevel modeling

72266c8

formatting the learning section

b93be6a

add anchors to notebooks

e5acf97

add anchors to all the main pages for easy intra-doc linking

604d16d

OriolAbril commented Nov 15, 2021

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martinacantaro and others added 2 commits November 16, 2021 01:49

Changelog

5e93f64

- Add information for institutions in the Contributing section - Center navbar - Split the About section into a main page with multiple subpages - Remove old reference to "developers" in the index toctree

fix anchor for Advanced_usage_of_Aesara_in_PyMC.rst

92bad68

Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com>

OriolAbril commented Nov 16, 2021

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OriolAbril mentioned this pull request Nov 18, 2021

Sphinx AutoSummary to automate API documentation #5082

Closed

4 tasks

martinacantaro added 2 commits November 21, 2021 19:25

redoing the community page after it got lost in a force push

6399b98

minor changes

101e9ea

martinacantaro linked an issue Nov 22, 2021 that may be closed by this pull request

Update sample code in the docs front page #5217

Closed

martinacantaro and others added 5 commits November 22, 2021 20:18

update code example

7ac3c16

redo community page

fa99d9e

try twitter feed on sidebar

dfa05bd

restructure contributing docs

6caabff

fix requirements

28d1701

OriolAbril marked this pull request as ready for review November 24, 2021 02:47

Apply suggestions from code review

8476e53

OriolAbril merged commit 99ec0ff into main Nov 24, 2021

larryshamalama mentioned this pull request Dec 9, 2021

Fixing PyMC Labs broken link in README #5251

Merged

OriolAbril deleted the doc_skeleton_update branch April 7, 2022 20:43

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[WIP] Reorganize and update documentation #5059

[WIP] Reorganize and update documentation #5059

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[WIP] Reorganize and update documentation #5059

[WIP] Reorganize and update documentation #5059

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